[Biococoa-dev] New Structure for BioCocoa

Alexander Griekspoor mek at mekentosj.com
Mon Jul 4 04:50:46 EDT 2005

About the IO discussion.
If we want a separate IO framework(s), I would suggest to keep all IO  
in one framework, the examples you give are all sequence related, so  
would depend only on the core framework (BCFoundation) right. If say  
the HMM framework would need some kind of special structure, than we  
can always opt to either define the structure in the foundation, but  
put all other stuff in the HMM framework, or place the HMM specific  
IO in the HMM framework as it is probably consists of only a few   
methods anyway.
But my main question is whether we really want to separate the IO  
framework as being independent. BCFoundation is so much related with  
IO that I don't really see a need to separate them. Most important, I  
don't think the IO will be so much code that it will be a large  
framework, or that it will make the foundation so bloated. It's two  
files right now! So why don't we make BCFoundation contain the IO  
like it does now. And the HMM framework contains its IO etc.
IMHO a basic core that defines sequences and can IO them doesn't have  
to be separated in two, I see it as one core. Similar to the fact  
that NSString can also IO them without the need of an IO framework.

On 4-jul-2005, at 1:20, Koen van der Drift wrote:

> On Jul 3, 2005, at 3:12 PM, Philipp Seibel wrote:
>> Sorry, but i got lost :-). I just meant that we can't put all io  
>> of all Frameworks in one IOFramework, because this IOFramework  
>> will then depend on all Frameworks ( Foundation ,HMM,  
>> Phylogenetics, etc.) because it will use the structure classes of  
>> all of them. To solve this problem, we will need a seperate  
>> IOFramework for each of the Frameworks.
> Aha, but now I understand :) I didn't realize that you were  
> assuming different data structures for each data format.  Maybe we  
> should put some effort in creating a general internal data format  
> that will also allow easy  exchange between the various formats.
> cheers,
> - Koen.
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                       ** Alexander Griekspoor **
                 The Netherlands Cancer Institute
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